fitodeMCMC-class

Class "fitodeMCMC".
Result of ode fitting based on Markov Chain Monte Carlo (MCMC)

Methods and functions for fitting ordinary differential equations (ODE) model in 'R'. Sensitivity equations are used to compute the gradients of ODE trajectories with respect to underlying parameters, which in turn allows for more stable fitting. Other fitting methods, such as MCMC (Markov chain Monte Carlo), are also available.

Sang Woo Park

fitode

Tools for Ordinary Differential Equations Model Fitting

Ben Bolker

fitodeMCMC-class function

<dl>
<dt><code>call</code></dt>
<dd>(languge) The call to <code>fitodeMCMC</code></dd></dl>
<dt><code>model</code></dt>
<dd>odemodel object</dd>
<dt><code>data</code></dt>
<dd>the time series data</dd>
<dt><code>coef</code></dt>
<dd>estimated parameters (posterior median)</dd>
<dt><code>vcov</code></dt>
<dd>estimated variance-covariance matrix</dd>
<dt><code>mcmc</code></dt>
<dd>mcmc.list object containing posterior samples</dd>
<dt><code>lp</code></dt>
<dd>mcmc.list object containing log-posterior values of posterior samples</dd>
<dt><code>link</code></dt>
<dd>list of link functions for model parameters</dd>
<dt><code>fixed</code></dt>
<dd>list of fixed parameters</dd>
<dt><code>prior</code></dt>
<dd>list of priors</dd>
<dt><code>details</code></dt>
<dd>a list containing miscellaneous objects for internal uses</dd>

Slots

Class "fitodeMCMC".
Result of ode fitting based on Markov Chain Monte Carlo (MCMC) — fitodeMCMC-class

<dl>
<dt><code>call</code></dt>
<dd>(languge) The call to <code>fitodeMCMC</code></dd>


<dt><code>model</code></dt>
<dd>odemodel object</dd>


<dt><code>data</code></dt>
<dd>the time series data</dd>


<dt><code>coef</code></dt>
<dd>estimated parameters (posterior median)</dd>


<dt><code>vcov</code></dt>
<dd>estimated variance-covariance matrix</dd>


<dt><code>mcmc</code></dt>
<dd>mcmc.list object containing posterior samples</dd>


<dt><code>lp</code></dt>
<dd>mcmc.list object containing log-posterior values of posterior samples</dd>


<dt><code>link</code></dt>
<dd>list of link functions for model parameters</dd>


<dt><code>fixed</code></dt>
<dd>list of fixed parameters</dd>


<dt><code>prior</code></dt>
<dd>list of priors</dd>


<dt><code>details</code></dt>
<dd>a list containing miscellaneous objects for internal uses</dd>


</dl>

fitodeMCMC-class: Class "fitodeMCMC". Result of ode fitting based on Markov Chain Monte Carlo (MCMC)

Description

Arguments

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